Only about 50 percent of the children have been covered . . . . . . . . the immunisation programme.

The correct answer is: against.

The preposition “against” is used to indicate protection from something. In this case, the children are being protected from diseases by being immunized.

The other prepositions could also be used in this sentence, but they would have different meanings.

• “By” could mean that the children were covered by the immunisation programme in the sense that they were included in it.
• “Through” could mean that the children were covered by the immunisation programme in the sense that they went through it.
• “In” could mean that the children were covered by the immunisation programme in the sense that they were inside it.

However, the preposition “against” is the most appropriate choice in this sentence because it conveys the meaning of protection most clearly.